Bivalent System of Deoxyribozymes for Efficient RNA Cleavage
The goal of gene therapy is to treat diseases through gene editing and modification of gene expression. Viral vectors, antisense oligonucleotides (ASO) and RNA interference (RNAi) are some of the gene therapies under development. DNAzymes, or deoxyribozymes (Dzs), are simple in design tools for RNA-...
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MDPI AG
2022-11-01
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| author | Michael Batsa Mikhail V. Dubovichenko Dmitry M. Kolpashchikov |
| author_facet | Michael Batsa Mikhail V. Dubovichenko Dmitry M. Kolpashchikov |
| author_sort | Michael Batsa |
| collection | DOAJ |
| description | The goal of gene therapy is to treat diseases through gene editing and modification of gene expression. Viral vectors, antisense oligonucleotides (ASO) and RNA interference (RNAi) are some of the gene therapies under development. DNAzymes, or deoxyribozymes (Dzs), are simple in design tools for RNA-cleaving and oligonucleotide-based gene therapy. However, Dz affinity and efficiency remain a significant challenge to be addressed. In nature, multiple ligands bind to targets at multiple sites with high affinity and avidity, resulting in effective inhibition or stimulation of biological responses. Scientists have reported multivalency in biological systems as a powerful strategy for achieving high-affinity molecular recognition. Our main goal was to improve the affinity and efficiency of DNAzyme in RNA cleaving by developing and optimizing 10-23 Dz base gene therapy molecules. We used 10-23 Dz to target folded mRNA and tested their knockdown efficiency in an in vitro physiological buffer. Next, we optimized 10-23 Dz by designing monovalent Dzs with varied arm lengths (short arms with 1–2 nucleotides less and long arms with 1–2 nucleotides more) to find the most efficient and stable construction and tested their efficiency in a cooperative association. It was observed that cooperative Dz1-Dz2 association was 3 times more efficient in comparison with separately working Dz1 and Dz2. Further investigation found that different lengths (−/+1, +2 nucleotides) of binding arms influenced the efficiency of 10-23 Dz. The result indicated that, as the length of the binding arms increased, the efficiency also increased. This research demonstrated that multivalent associations of DNAzymes have great potential to increase DNAzyme-cleaving RNA affinity and efficiency as a therapeutic agent. |
| first_indexed | 2024-03-11T06:51:53Z |
| format | Article |
| id | doaj.art-bd44a030248a4fa7b284d281a70a0b33 |
| institution | Directory Open Access Journal |
| issn | 2673-9976 |
| language | English |
| last_indexed | 2024-03-11T06:51:53Z |
| publishDate | 2022-11-01 |
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| series | Biology and Life Sciences Forum |
| spelling | doaj.art-bd44a030248a4fa7b284d281a70a0b332023-11-17T09:55:37ZengMDPI AGBiology and Life Sciences Forum2673-99762022-11-01201610.3390/IECBM2022-13510Bivalent System of Deoxyribozymes for Efficient RNA CleavageMichael Batsa0Mikhail V. Dubovichenko1Dmitry M. Kolpashchikov2Laboratory of Molecular Robotics and Biosensor Materials, Solution Chemistry of Advanced Materials and Technologies (SCAMT) Institute, ITMO University, 197101 Saint Petersburg, RussiaLaboratory of Molecular Robotics and Biosensor Materials, Solution Chemistry of Advanced Materials and Technologies (SCAMT) Institute, ITMO University, 197101 Saint Petersburg, RussiaLaboratory of Molecular Robotics and Biosensor Materials, Solution Chemistry of Advanced Materials and Technologies (SCAMT) Institute, ITMO University, 197101 Saint Petersburg, RussiaThe goal of gene therapy is to treat diseases through gene editing and modification of gene expression. Viral vectors, antisense oligonucleotides (ASO) and RNA interference (RNAi) are some of the gene therapies under development. DNAzymes, or deoxyribozymes (Dzs), are simple in design tools for RNA-cleaving and oligonucleotide-based gene therapy. However, Dz affinity and efficiency remain a significant challenge to be addressed. In nature, multiple ligands bind to targets at multiple sites with high affinity and avidity, resulting in effective inhibition or stimulation of biological responses. Scientists have reported multivalency in biological systems as a powerful strategy for achieving high-affinity molecular recognition. Our main goal was to improve the affinity and efficiency of DNAzyme in RNA cleaving by developing and optimizing 10-23 Dz base gene therapy molecules. We used 10-23 Dz to target folded mRNA and tested their knockdown efficiency in an in vitro physiological buffer. Next, we optimized 10-23 Dz by designing monovalent Dzs with varied arm lengths (short arms with 1–2 nucleotides less and long arms with 1–2 nucleotides more) to find the most efficient and stable construction and tested their efficiency in a cooperative association. It was observed that cooperative Dz1-Dz2 association was 3 times more efficient in comparison with separately working Dz1 and Dz2. Further investigation found that different lengths (−/+1, +2 nucleotides) of binding arms influenced the efficiency of 10-23 Dz. The result indicated that, as the length of the binding arms increased, the efficiency also increased. This research demonstrated that multivalent associations of DNAzymes have great potential to increase DNAzyme-cleaving RNA affinity and efficiency as a therapeutic agent.https://www.mdpi.com/2673-9976/20/1/6bivalent systemdeoxyribozymesDNAzymesgene therapybiomolecules |
| spellingShingle | Michael Batsa Mikhail V. Dubovichenko Dmitry M. Kolpashchikov Bivalent System of Deoxyribozymes for Efficient RNA Cleavage Biology and Life Sciences Forum bivalent system deoxyribozymes DNAzymes gene therapy biomolecules |
| title | Bivalent System of Deoxyribozymes for Efficient RNA Cleavage |
| title_full | Bivalent System of Deoxyribozymes for Efficient RNA Cleavage |
| title_fullStr | Bivalent System of Deoxyribozymes for Efficient RNA Cleavage |
| title_full_unstemmed | Bivalent System of Deoxyribozymes for Efficient RNA Cleavage |
| title_short | Bivalent System of Deoxyribozymes for Efficient RNA Cleavage |
| title_sort | bivalent system of deoxyribozymes for efficient rna cleavage |
| topic | bivalent system deoxyribozymes DNAzymes gene therapy biomolecules |
| url | https://www.mdpi.com/2673-9976/20/1/6 |
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